Ok so i just meddled with this for a bit and found a way that worked for me since I couldn't figure out mobi2mobi (running mac osx 10.6.3)
All I did was use calibre to transfer whatever file to mobi, and picked my cover image.
were going to pretend the name of my book was title.
Once I got the title.mobi file and the cover.jpg i tried something stupid. I changed the file name of "cover.jpg" to "title.mbp" and used iphone explorer to put both of them into the ebook folder as described above.
and odd enough it worked! repeated for a few ebooks to verify. Try it out and let me know if it works for you!